HHsearch alignment for GI: 254780818 and conserved domain: pfam04857
>pfam04857 CAF1 CAF1 family ribonuclease. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localizes to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom#resolution.
Probab=98.23 E-value=2.3e-06 Score=59.74 Aligned_cols=166 Identities=20% Similarity=0.261 Sum_probs=92.5
Q ss_pred CCEEEEECCCCCCCCC-----C--------------C--EEEEEEEEEEE-CCEECC--CE--EEEE-ECCCCCCCCHHH
Q ss_conf 7589998467888888-----8--------------8--89999999999-998803--13--7989-858882288657
Q gi|254780818|r 7 MRKIVFDIETTGLDSK-----N--------------D--RIIEIGAVELL-DYSKTN--RT--FQVF-LCPNGRKNSPEA 59 (245)
Q Consensus 7 mr~iv~D~ETTGl~~~-----~--------------d--~Iieigav~i~-~~~~~~--~~--f~~~-i~P~~~~i~~~~ 59 (245)
T Consensus 22 ~~fVaiDtEFpG~v~~p~~~~~~t~~~~Y~~lk~nVd~l~iiQlGlt~~~~~g~~p~~~~~wqfNf~~F~~~~d~~~~~S 101 (235)
T pfam04857 22 YDFIAIDTEFPGVVARPIGSFRSTSDYRYQALRKNVDRLKIIQLGLTLFDEKGNLPDSYYTWQFNFSLFNLEEDFYAPSS 101 (235)
T ss_pred CCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCCCHHH
T ss_conf 99899951427524689888889878999999843001231468988874688789874378501556797322116889
Q ss_pred E---EECCCCCCCC-CCCCC---CCHHHHHHHH-HHHCCCCEEEEECCCCCCCEEEECHHCCCCCC----------CCCC
Q ss_conf 2---4202101232-24852---1002344777-53002320231023224311210000011222----------2100
Q gi|254780818|r 60 L---KLHGITDEFL-KDKPS---FSSIFSEFWD-FFNEQNAEWIAHNAKFDVGFINAELQRINKDP----------LDPS 121 (245)
Q Consensus 60 ~---~ihGIt~~~l-~~~p~---f~ev~~~f~~-fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~----------~~~~ 121 (245)
T Consensus 102 i~fL~~~G~DF~~~~~~GI~~~~f~e~l~~-S~lv~~~~~~~wv~f~g~yD~~yl~k~l~g~~LP~~~~eF~~~l~~~FP 180 (235)
T pfam04857 102 IEFLAKQGFDFNKHRREGIPYLRFAELLGS-SGLFLNISSVTWVTFHGLYDFGYLLKLLTGGPLPETLDDFLELLRELFP 180 (235)
T ss_pred HHHHHHCCCCHHHHHHHCCCHHHHHHHHHH-HHHEECCCCCEEEEECCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCC
T ss_conf 999998598889998709998999989987-0302057998799817277899999997499899989999999999777
Q ss_pred HHCCCHHCCCCCC---CCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 0011000000017---764222378999718754555666402699999999999
Q gi|254780818|r 122 RIIDTLSIARRKH---PSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIK 173 (245)
Q Consensus 122 ~~iDTl~lar~~~---p~~~~~L~~l~~~~~i~~~~r~~H~Al~Da~~~a~v~~~ 173 (245)
T Consensus 181 ~vyD~K~la~~~~~~~~~~~~gL~~lA~~L~v~r~~g~~HqAGsDSllT~~~F~k 235 (235)
T pfam04857 181 RVYDTKYLAKFCFELDGGSNGGLQELADLLGVNRRVGRLHQAGSDSLLTALVFFK 235 (235)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHC
T ss_conf 1750999998522135875578999999749978889866655299999987619